TimiRGeN

DOI: 10.18129/B9.bioc.TimiRGeN    

This is the development version of TimiRGeN; to use it, please install the devel version of Bioconductor.

Time sensitive microRNA-mRNA integration, analysis and network generation tool

Bioconductor version: Development (3.12)

TimiRGeN (Time Incorporated miR-mRNA Generation of Networks) is a novel R package which functionally analyses and integrates time course miRNA-mRNA differential expression data. This tool can generate small networks within R or export results into cytoscape or pathvisio for more detailed network construction and hypothesis generation. This tool is created for researchers that wish to dive deep into time series multi-omic datasets. TimiRGeN goes further than many other tools in terms of data reduction. Here, potentially hundreds of thousands of potential miRNA-mRNA interactions can be whittled down into a handful of high confidence miRNA-mRNA interactions effecting a signalling pathway, across a time course.

Author: Krutik Patel [aut, cre]

Maintainer: Krutik Patel <K.Patel5 at newcastle.ac.uk>

Citation (from within R, enter citation("TimiRGeN")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("TimiRGeN")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TimiRGeN")

 

HTML R Script TimiRGeN
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, Network, Pathways, Software, TimeCourse, Visualization, miRNA
Version 0.99.4159
In Bioconductor since BioC 3.12 (R-4.0)
License GPL-3
Depends R (>= 4.0), Mfuzz, MultiAssayExperiment
Imports biomaRt, clusterProfiler, dplyr (>= 0.8.4), gtools (>= 3.8.1), ggplot2, graphics, grDevices, igraph (>= 1.2.4.2), RCy3, readxl, rWikiPathways, stats, tidyr (>= 1.0.2), stringr (>= 1.4.0)
LinkingTo
Suggests BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db, org.Mm.eg.db, testthat (>= 2.3.1)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TimiRGeN_0.99.4159.tar.gz
Windows Binary TimiRGeN_0.99.4159.zip
macOS 10.13 (High Sierra) TimiRGeN_0.99.4159.tgz
Source Repository git clone https://git.bioconductor.org/packages/TimiRGeN
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TimiRGeN
Package Short Url https://bioconductor.org/packages/TimiRGeN/
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